Thanks for your reply Douglas,

I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer?

Thanks

-Hedyeh

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Date: Tue, 17 Apr 2018 11:49:04 -0400
From: Douglas Greve <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Non-rigid registration approaches
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <763da2ef-359a-9f44-9b54-1f96acb3b2ef@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Not really. Are you trying to account for B0 distortion in the DTI? If
you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to
account for it

On 4/16/18 10:29 AM, Hedyeh Javaheri wrote:
> Hello all,
>
> I am performing DTI analysis and wanted to know if Freesurfer has a
> tool for non-rigid registration.
> I performed recon-all and dt_recon on my subject and then used the
> register.dat file that was generated by dt_recon to convert the
> dt_recon output files back into the space of my orig.nii file from the
> recon-all output. Now I need to register the files in the orig.nii
> space back onto the T1 MRI that is in native space.
>
> I have tried using? mri_vol2vol to get the files in the orig.nii
> (recon-all) space into the T1 native space without using a
> registration file (I used --regheader) and now the registration matrix
> of my file is the same as the native space, but when I use rview to
> visualize the registration there are flaws. I've also tried this
> co-registration using tkregister2 to create a registration file called
> register.native.dat, and then used mri_vol2vol with
> register.native.dat; and the results were the same as when I used
> mri_vol2vol with --regheader.
>
> Is there a tool to do actual manual registration in Freesurfer? Using
> tkregister2 I cannot perform localized changes; and the global changes
> it is capable of do not improve on the coregistration.
>
> Here is a breakdown of what I have done:
>
> subject in Native space to Freesurfer conformed space using recon-all,
> output: orig.nii
> subject in Native space to other Freesurfer space using dt_recon,
> output: lowb.nii and register.dat
> From the other Freesufer space to Freesurfer conformed space using
> register.dat, output: lowb2orig.nii
> attempting to convert from Freesurfer conformed space to Native space:
> ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration
> ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then
> mri_vol2vol and ?register.native.dat --> poor registration
>
> I am running Freesurfer version 6 on Windows.
>
> Thanks in advance!
> -Hedyeh Javaheri